Variant report

Variant	rs6504622
Chromosome Location	chr17:45019731-45019732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45019717..45021818-chr17:45023982..45025804,3	MCF-7	breast:
2	chr17:45016816..45019749-chr17:45021342..45024491,3	K562	blood:
3	chr17:45019636..45020289-chr17:45077991..45079169,4	MCF-7	breast:
4	chr17:45000610..45002133-chr17:45017223..45020134,3	MCF-7	breast:
5	chr17:44928815..44931098-chr17:45016845..45019824,2	K562	blood:
6	chr17:45017959..45019957-chr17:45020327..45022485,3	MCF-7	breast:
7	chr17:44953449..44954379-chr17:45019200..45020186,2	MCF-7	breast:
8	chr17:44998043..45003369-chr17:45017156..45021990,5	K562	blood:
9	chr17:44998974..45001797-chr17:45018789..45021096,2	MCF-7	breast:
10	chr17:45016499..45018728-chr17:45019310..45022660,4	MCF-7	breast:
11	chr17:45012485..45015946-chr17:45019654..45022086,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000262633	Chromatin interaction
ENSG00000210709	Chromatin interaction
ENSG00000261886	Chromatin interaction
ENSG00000158955	Chromatin interaction
ENSG00000108433	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1047779	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052504	1.00[ASN][1000 genomes]
rs1052586	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10853085	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10853087	1.00[ASN][1000 genomes]
rs11079742	0.85[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs11079745	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11079750	0.84[CEU][hapmap]
rs11652318	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11654971	1.00[ASN][1000 genomes]
rs11655668	0.86[JPT][hapmap]
rs11656362	0.99[ASN][1000 genomes]
rs11658276	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11869840	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601886	1.00[ASN][1000 genomes]
rs12940071	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618989	0.99[ASN][1000 genomes]
rs1623402	1.00[ASN][1000 genomes]
rs1662576	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1662577	1.00[ASN][1000 genomes]
rs1662594	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1662596	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1662597	0.98[ASN][1000 genomes]
rs17608961	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1838105	0.82[JPT][hapmap]
rs1867237	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs189899	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs197912	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs197913	0.89[ASN][1000 genomes]
rs197915	0.92[ASN][1000 genomes]
rs197917	0.99[ASN][1000 genomes]
rs197918	1.00[ASN][1000 genomes]
rs197919	1.00[ASN][1000 genomes]
rs197922	0.82[JPT][hapmap]
rs197923	0.82[JPT][hapmap]
rs197925	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs197926	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2003538	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2003539	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072317	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2191033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2316330	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2317997	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28553405	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2920396	1.00[ASN][1000 genomes]
rs2920397	1.00[ASN][1000 genomes]
rs35707546	0.98[ASN][1000 genomes]
rs3760377	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785888	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785889	0.85[CEU][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs3809854	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851784	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851785	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851786	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851787	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851792	0.83[CEU][hapmap]
rs4074249	0.84[CEU][hapmap]
rs4381655	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4602097	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968248	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4968250	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968285	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968287	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968288	1.00[ASN][1000 genomes]
rs4968290	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968304	0.84[CEU][hapmap]
rs61671555	0.83[EUR][1000 genomes]
rs62075889	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62075896	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7213526	0.99[ASN][1000 genomes]
rs7216991	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7225428	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7342957	1.00[ASN][1000 genomes]
rs736603	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs736604	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs740617	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758391	0.85[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs758392	0.85[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9303532	0.83[EUR][1000 genomes]
rs9889741	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9893713	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9898527	0.83[EUR][1000 genomes]
rs9898981	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9901977	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9910899	0.83[EUR][1000 genomes]
rs9911366	0.83[EUR][1000 genomes]
rs9911967	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9912794	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv428672	chr17:44872446-45023425	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6504622	PLCD3	cis	parietal	SCAN
rs6504622	LRRC46	cis	parietal	SCAN
rs6504622	NSF	cis	lymphoblastoid	seeQTL
rs6504622	C17orf53	cis	parietal	SCAN
rs6504622	GOSR2	cis	multi-tissue	Pritchard
rs6504622	MYL4	cis	multi-tissue	Pritchard
rs6504622	GOSR2	cis	normal skin	skin_eQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45001600-45020800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:45002000-45021000	Weak transcription	Fetal Heart	heart
3	chr17:45002800-45020000	Strong transcription	Fetal Muscle Leg	muscle
4	chr17:45005000-45019800	Strong transcription	GM12878-XiMat	blood
5	chr17:45005600-45020200	Strong transcription	Fetal Thymus	thymus
6	chr17:45005800-45019800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr17:45005800-45020000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr17:45006200-45020000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr17:45006600-45019800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr17:45006800-45019800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:45006800-45020000	Strong transcription	Dnd41	blood
12	chr17:45007000-45019800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr17:45007000-45019800	Strong transcription	HSMM	muscle
14	chr17:45007600-45020000	Strong transcription	A549	lung
15	chr17:45007800-45019800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:45009200-45019800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr17:45009800-45019800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:45012800-45040000	Weak transcription	Hela-S3	cervix
19	chr17:45013400-45020200	Weak transcription	Fetal Brain Male	brain
20	chr17:45013600-45019800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:45014000-45020000	Strong transcription	Lung	lung
22	chr17:45014000-45020200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:45014000-45020200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr17:45014000-45020600	Weak transcription	Right Atrium	heart
25	chr17:45014200-45020800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr17:45014400-45020400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr17:45016800-45021000	Weak transcription	Fetal Kidney	kidney
28	chr17:45017200-45020000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr17:45017200-45020800	Weak transcription	Psoas Muscle	Psoas
30	chr17:45017400-45019800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr17:45017400-45020200	Weak transcription	Brain Substantia Nigra	brain
32	chr17:45017400-45021200	Weak transcription	Small Intestine	intestine
33	chr17:45017600-45020200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr17:45017600-45020400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr17:45017600-45020800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr17:45017800-45019800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr17:45017800-45020200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr17:45018000-45019800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr17:45018000-45020200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr17:45018000-45020200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr17:45018000-45020200	Weak transcription	Brain Hippocampus Middle	brain
42	chr17:45018000-45020600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:45018000-45020600	Weak transcription	Ovary	ovary
44	chr17:45018000-45020800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr17:45018000-45026000	Weak transcription	Primary B cells from cord blood	blood
46	chr17:45018200-45019800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr17:45018200-45019800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr17:45018200-45019800	Weak transcription	Placenta	Placenta
49	chr17:45018200-45020000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr17:45018200-45020000	Weak transcription	Brain Cingulate Gyrus	brain

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